# do not use this module directly # See Bio::Map::Mappable for an example of # implementation.

Description

This object handles the generic notion of an element placed on a(linear) Map. A Mappable can have multiple positions in multiple maps, such asis the case of Restriction enzyme cut sites on sequence maps. For exactinformation about a mappable's position in a map one must query the associatePositionI objects which are accessible through the get_positions() method.

Title : get_positions Usage : my @positions = $mappable->get_positions(); Function: Get all the Positions of this Mappable (sorted). Returns : Array of Bio::Map::PositionI objects Args : none for all, ORBio::Map::MapI object for positions on the given map, AND/OR some other true value to avoid sorting

Title : purge_positions Usage : $mappable->purge_positions(); Function: Remove positions from this mappable. Returns : n/a Args : none to remove all positions, ORBio::Map::PositionI object to remove just that Position, ORBio::Map::MapI object to remove only those positions on the given map

Title : name Usage : my $name = $marker->name(); $marker->name($new_name); Function: Get/Set the name for this Mappable. Returns : A scalar representing the current name of this Mappable Args : none to get string to set

Title : id Usage : my $id = $marker->id(); $marker->id($new_id); Function: Get/Set the id for this Mappable. Returns : A scalar representing the current id of this Mappable Args : none to get string to set

Title : equals Usage : if ($mappable->equals($other_mappable)) {...} my @equal_positions = $mappable->equals($other_mappable); Function: Finds the positions in this mappable that are equal to any comparison positions. Returns : array of Bio::Map::PositionI objects Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare this one to (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to ask if the Positions equal in terms of their relative position to the thing described by that Relative

Title : overlaps Usage : if ($mappable->overlaps($other_mappable)) {...} my @overlapping_positions = $mappable->overlaps($other_mappable); Function: Finds the positions in this mappable that overlap with any comparison positions. Returns : array of Bio::Map::PositionI objects Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare this one to (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to ask if the Positions overlap in terms of their relative position to the thing described by that Relative

Title : contains Usage : if ($mappable->contains($other_mappable)) {...} my @container_positions = $mappable->contains($other_mappable); Function: Finds the positions in this mappable that contain any comparison positions. Returns : array of Bio::Map::PositionI objects Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare this one to (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to ask if the Positions contains in terms of their relative position to the thing described by that Relative

Title : intersection Usage : my $position = $mappable->intersection($other_mappable); my $position = Bio::Map::Mappable->intersection(\@mappables); Function: Make the position that is at the intersection of all positions of all supplied mappables. Returns : Bio::Map::PositionI object or undef (if not all positions overlap) Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to to ask how the Positions intersect in terms of their relative position to the thing described by that Relative

Title : union Usage : my $position = $mappable->union($other_mappable); my $position = Bio::Map::Mappable->union(@mappables); Function: Make the minimal position that contains all of the positions of all supplied mappables. Returns : Bio::Map::PositionI object or undef (if not all positions overlap) Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, the key => value pairs below -map => Bio::Map::MapI : optionally a Map to only consider positions on the given map -relative => Bio::Map::RelativeI : optionally a Relative to to ask if the union of the Positions in terms of their relative position to the thing described by that Relative

Please direct usage questions or support issues to the mailing list:bioperl-l@bioperl.orgrather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.